9CGN

Pikromycin Thioesterase with heptaketide adduct

• PDB DOI: https://doi.org/10.2210/pdb9CGN/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces venezuelae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-06-30 Released: 2024-09-18 
• Deposition Author(s): Smith, J.L., Choudhary, V.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.252 
• R-Value Work: 0.174 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Substrate Trapping in Polyketide Synthase Thioesterase Domains: Structural Basis for Macrolactone Formation

McCullough, T.M., Choudhary, V., Akey, D.L., Skiba, M.A., Bernard, S.M., Kittendorf, J.D., Schmidt, J.J., Sherman, D.H., Smith, J.L.

(2024) ACS Catal 14

• DOI: https://doi.org/10.1021/acscatal.4c03637

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.22 kDa 
• Atom Count: 4,290 
• Modelled Residue Count: 554 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Narbonolide/10-deoxymethynolide synthase PikA4, module 6	A, B	283	Streptomyces venezuelae	Mutation(s): 1  Gene Names: pikAIV EC: 2.3.1.239 (PDB Primary Data), 2.3.1.240 (PDB Primary Data)
UniProt
Find proteins for Q9ZGI2 (Streptomyces venezuelae) Explore Q9ZGI2  Go to UniProtKB:  Q9ZGI2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AWF (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2S,4R,5S,6S,8R,12R,13R)-5,13-dihydroxy-2,4,6,8,12-pentamethyl-3,9-dioxopentadecanal C20 H36 O5 LWRZYDNPGZEYIZ-AEUCKGDRSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DPP	A, B	L-PEPTIDE LINKING	C3 H8 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.252 
• R-Value Work: 0.174 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.04	α = 90
b = 105.18	β = 90
c = 114.58	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-18 
Deposition Author(s): Smith, J.L., Choudhary, V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01 DK042303

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release